Plectorhinchus orientalis and Plectorhinchus vittatus were two species of colorful coral reef sweetlips which distribute in the areas of Indo-Western Pacific. The two species have long been considered as a synonym (oriental sweetlips) in morphology. In order to investigate the validity of two species at the molecular level, complete mitochondrial genomes of the two species were first determined. The genomes were 16,546 bp (P. orientalis) and 16,545 bp (P. vittatus) in size, respectively, which both consisted of a typical structure of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and one noncoding control region. Genomic composition, organization and gene order were similar to that obtained in most vertebrates. By comparative analysis of the two genomes, 941 variable sites (5.69%) were found. Sequence divergences of 13 protein-coding genes, 2 rRNA genes and one control region which are commonly used as molecular markers between the two species ranged from 2.4% (12S rRNA) to 11.2% (ND6), all divergence values were larger than 2%. Great variations of Cyt b and COI between P. orientalis and P. vittatus were revealed to be 6.0% and 7.4%, respectively, which were largely greater than the threshold of species diagnosis divergence value of 2%. Inner individual divergence values of each species were less than 0.5%. In the molecular phylogenetic trees, the longer branch length also clearly distinguished the independent placement of the two species. These results revealed great genetic differences between P. orientalis and P. vittatus, and strongly suggested that they might be two distinct species and should not be placed as synonym.